Flat-field correction (without detector plane handling)

6 files changed, 437 insertions, 0 deletions

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 116b400..bbbc5fb 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -5,6 +5,7 @@ set(ufofilter_SRCS
     ufo-roof-read-task.c
     ufo-roof-build-task.c
     ufo-roof-filter-task.c
+    ufo-roof-flat-field-correct.c
     )
 
 set(common_SRCS
diff --git a/src/kernels/meson.build b/src/kernels/meson.build
index 9803fb9..6472953 100644
--- a/src/kernels/meson.build
+++ b/src/kernels/meson.build
@@ -1,4 +1,5 @@
 kernel_files = [
+    'roof-ffc.cl'
 ]
 
 install_data(kernel_files,
diff --git a/src/kernels/roof-ffc.cl b/src/kernels/roof-ffc.cl
new file mode 100644
index 0000000..8752990
--- /dev/null
+++ b/src/kernels/roof-ffc.cl
@@ -0,0 +1,52 @@
+/*
+ * Copyright (C) 2011-2013 Karlsruhe Institute of Technology
+ *
+ * This file is part of Ufo.
+ *
+ * This library is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+kernel void
+flat_correct (global float *corrected,
+              global float *data,
+              global const float *dark,
+              global const float *flat,
+              const int sinogram_input,
+              const int absorptivity,
+              const int fix_abnormal,
+              const float dark_scale,
+              const float flat_scale)
+{
+    const float eps = 1E-5;
+    const int gid = get_global_id(1) * get_global_size(0) + get_global_id(0);
+    const int corr_idx = sinogram_input ? get_global_id(0) : gid;
+    const float cdark = dark[corr_idx] * dark_scale;
+    const float cflat = flat[corr_idx] * flat_scale;
+    float result;
+
+    float nom = data[gid] - cdark;
+    float denom = cflat - cdark;
+
+    if (nom < eps) nom = eps;
+//    if (denom < eps) denom = eps;
+    if (denom < eps) denom = eps;
+    
+    result = -log(nom / denom);
+
+    if (fix_abnormal && (isnan (result) || isinf (result))) {
+        result = 0.0f;
+    }
+
+    corrected[gid] = result;
+}
diff --git a/src/meson.build b/src/meson.build
index 8f8930a..324c744 100644
--- a/src/meson.build
+++ b/src/meson.build
@@ -2,6 +2,7 @@ plugins = [
     'roof-read',
     'roof-build',
     'roof-filter',
+    'roof-flat-field-correct'
 ]
 
 roof_common_src = [
diff --git a/src/ufo-roof-flat-field-correct-task.c b/src/ufo-roof-flat-field-correct-task.c
new file mode 100644
index 0000000..7c1f9dc
--- /dev/null
+++ b/src/ufo-roof-flat-field-correct-task.c
@@ -0,0 +1,315 @@
+/*
+ * Copyright (C) 2011-2013 Karlsruhe Institute of Technology
+ *
+ * This file is part of Ufo.
+ *
+ * This library is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifdef __APPLE__
+#include <OpenCL/cl.h>
+#else
+#include <CL/cl.h>
+#endif
+#include <math.h>
+#include "ufo-roof-flat-field-correct-task.h"
+
+
+struct _UfoRoofFlatFieldCorrectTaskPrivate {
+    gboolean fix_nan_and_inf;
+    gboolean absorptivity;
+    gboolean sinogram_input;
+    gfloat dark_scale;
+    gfloat flat_scale;
+    cl_kernel kernel;
+};
+
+static void ufo_task_interface_init (UfoTaskIface *iface);
+
+G_DEFINE_TYPE_WITH_CODE (UfoRoofFlatFieldCorrectTask, ufo_roof_flat_field_correct_task, UFO_TYPE_TASK_NODE,
+                         G_IMPLEMENT_INTERFACE (UFO_TYPE_TASK,
+                                                ufo_task_interface_init))
+
+#define UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE(obj) (G_TYPE_INSTANCE_GET_PRIVATE((obj), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK, UfoRoofFlatFieldCorrectTaskPrivate))
+
+enum {
+    PROP_0,
+    PROP_FIX_NAN_AND_INF,
+    PROP_ABSORPTIVITY,
+    PROP_SINOGRAM_INPUT,
+    PROP_DARK_SCALE,
+    PROP_FLAT_SCALE,
+    N_PROPERTIES
+};
+
+static GParamSpec *properties[N_PROPERTIES] = { NULL, };
+
+UfoNode *
+ufo_roof_flat_field_correct_task_new (void)
+{
+    return UFO_NODE (g_object_new (UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK, NULL));
+}
+
+static void
+ufo_roof_flat_field_correct_task_setup (UfoTask *task,
+                                   UfoResources *resources,
+                                   GError **error)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv;
+
+    priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (task);
+    priv->kernel = ufo_resources_get_kernel (resources, "roof-ffc.cl", "flat_correct", NULL, error);
+
+    if (priv->kernel)
+        UFO_RESOURCES_CHECK_SET_AND_RETURN (clRetainKernel (priv->kernel), error);
+}
+
+static void
+ufo_roof_flat_field_correct_task_get_requisition (UfoTask *task,
+                                             UfoBuffer **inputs,
+                                             UfoRequisition *requisition,
+                                             GError **error)
+{
+    ufo_buffer_get_requisition (inputs[0], requisition);
+
+    if (ufo_buffer_cmp_dimensions (inputs[1], requisition) != 0 ||
+        ufo_buffer_cmp_dimensions (inputs[2], requisition) != 0) {
+        g_set_error_literal (error, UFO_TASK_ERROR, UFO_TASK_ERROR_GET_REQUISITION,
+                             "flat-field-correct inputs must have the same size");
+    }
+}
+
+static guint
+ufo_roof_flat_field_correct_task_get_num_inputs (UfoTask *task)
+{
+    return 3;
+}
+
+static guint
+ufo_roof_flat_field_correct_task_get_num_dimensions (UfoTask *task, guint input)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv;
+
+    priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (task);
+    g_return_val_if_fail (input <= 2, 0);
+
+    /* A sinogram */
+    if (input == 0)
+        return 2;
+
+    /* A row of dark frame depend on the sinogram_input flag */
+    return priv->sinogram_input ? 1 : 2;
+}
+
+static UfoTaskMode
+ufo_roof_flat_field_correct_task_get_mode (UfoTask *task)
+{
+    return UFO_TASK_MODE_PROCESSOR | UFO_TASK_MODE_GPU;
+}
+
+static gboolean
+ufo_roof_flat_field_correct_task_process (UfoTask *task,
+                                        UfoBuffer **inputs,
+                                        UfoBuffer *output,
+                                        UfoRequisition *requisition)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv;
+    UfoProfiler *profiler;
+    UfoGpuNode *node;
+
+    cl_command_queue cmd_queue;
+    cl_mem proj_mem;
+    cl_mem dark_mem;
+    cl_mem flat_mem;
+    cl_mem out_mem;
+    gint absorptivity, sino_in, fix_nan_and_inf;
+
+    node = UFO_GPU_NODE (ufo_task_node_get_proc_node (UFO_TASK_NODE (task)));
+    cmd_queue = ufo_gpu_node_get_cmd_queue (node);
+    proj_mem = ufo_buffer_get_device_array (inputs[0], cmd_queue);
+    dark_mem = ufo_buffer_get_device_array (inputs[1], cmd_queue);
+    flat_mem = ufo_buffer_get_device_array (inputs[2], cmd_queue);
+    out_mem = ufo_buffer_get_device_array (output, cmd_queue);
+
+    priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (task);
+    absorptivity = (gint) priv->absorptivity;
+    sino_in = (gint) priv->sinogram_input;
+    fix_nan_and_inf = (gint) priv->fix_nan_and_inf;
+
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 0, sizeof (cl_mem), &out_mem));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 1, sizeof (cl_mem), &proj_mem));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 2, sizeof (cl_mem), &dark_mem));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 3, sizeof (cl_mem), &flat_mem));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 4, sizeof (cl_int), &sino_in));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 5, sizeof (cl_int), &absorptivity));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 6, sizeof (cl_int), &fix_nan_and_inf));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 7, sizeof (cl_float), &priv->dark_scale));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 8, sizeof (cl_float), &priv->flat_scale));
+
+    profiler = ufo_task_node_get_profiler (UFO_TASK_NODE (task));
+    ufo_profiler_call (profiler, cmd_queue, priv->kernel, 2, requisition->dims, NULL);
+
+    return TRUE;
+}
+
+static void
+ufo_roof_flat_field_correct_task_set_property (GObject *object,
+                                             guint property_id,
+                                             const GValue *value,
+                                             GParamSpec *pspec)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (object);
+
+    switch (property_id) {
+        case PROP_FIX_NAN_AND_INF:
+            priv->fix_nan_and_inf = g_value_get_boolean (value);
+            break;
+        case PROP_ABSORPTIVITY:
+            priv->absorptivity = g_value_get_boolean (value);
+            break;
+        case PROP_SINOGRAM_INPUT:
+            priv->sinogram_input = g_value_get_boolean (value);
+            break;
+        case PROP_DARK_SCALE:
+            priv->dark_scale = g_value_get_float (value);
+            break;
+        case PROP_FLAT_SCALE:
+            priv->flat_scale = g_value_get_float (value);
+            break;
+
+        default:
+            G_OBJECT_WARN_INVALID_PROPERTY_ID (object, property_id, pspec);
+            break;
+    }
+}
+
+static void
+ufo_roof_flat_field_correct_task_get_property (GObject *object,
+                                             guint property_id,
+                                             GValue *value,
+                                             GParamSpec *pspec)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (object);
+
+    switch (property_id) {
+        case PROP_FIX_NAN_AND_INF:
+            g_value_set_boolean (value, priv->fix_nan_and_inf);
+            break;
+        case PROP_ABSORPTIVITY:
+            g_value_set_boolean (value, priv->absorptivity);
+            break;
+        case PROP_SINOGRAM_INPUT:
+            g_value_set_boolean (value, priv->sinogram_input);
+            break;
+        case PROP_DARK_SCALE:
+            g_value_set_float (value, priv->dark_scale);
+            break;
+        case PROP_FLAT_SCALE:
+            g_value_set_float (value, priv->flat_scale);
+            break;
+        default:
+            G_OBJECT_WARN_INVALID_PROPERTY_ID (object, property_id, pspec);
+            break;
+    }
+}
+
+static void
+ufo_roof_flat_field_correct_task_finalize (GObject *object)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv;
+
+    priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (object);
+
+    if (priv->kernel) {
+        UFO_RESOURCES_CHECK_CLERR (clReleaseKernel (priv->kernel));
+        priv->kernel = NULL;
+    }
+
+    G_OBJECT_CLASS (ufo_roof_flat_field_correct_task_parent_class)->finalize (object);
+}
+
+static void
+ufo_task_interface_init (UfoTaskIface *iface)
+{
+    iface->setup = ufo_roof_flat_field_correct_task_setup;
+    iface->get_num_inputs = ufo_roof_flat_field_correct_task_get_num_inputs;
+    iface->get_num_dimensions = ufo_roof_flat_field_correct_task_get_num_dimensions;
+    iface->get_mode = ufo_roof_flat_field_correct_task_get_mode;
+    iface->get_requisition = ufo_roof_flat_field_correct_task_get_requisition;
+    iface->process = ufo_roof_flat_field_correct_task_process;
+}
+
+static void
+ufo_roof_flat_field_correct_task_class_init (UfoRoofFlatFieldCorrectTaskClass *klass)
+{
+    GObjectClass *gobject_class = G_OBJECT_CLASS (klass);
+
+    gobject_class->set_property = ufo_roof_flat_field_correct_task_set_property;
+    gobject_class->get_property = ufo_roof_flat_field_correct_task_get_property;
+    gobject_class->finalize = ufo_roof_flat_field_correct_task_finalize;
+
+    properties[PROP_FIX_NAN_AND_INF] =
+        g_param_spec_boolean("fix-nan-and-inf",
+            "Replace NAN and INF values with 0.0",
+            "Replace NAN and INF values with 0.0",
+            FALSE,
+            G_PARAM_READWRITE);
+
+/*
+    properties[PROP_ABSORPTIVITY] =
+        g_param_spec_boolean ("absorption-correct",
+            "Absorption correct",
+            "Absorption correct",
+            FALSE,
+            G_PARAM_READWRITE);
+
+    properties[PROP_SINOGRAM_INPUT] =
+        g_param_spec_boolean ("sinogram-input",
+            "If sinogram-input is True we correct only one line (the sinogram), thus darks are flats are 1D",
+            "If sinogram-input is True we correct only one line (the sinogram), thus darks are flats are 1D",
+            FALSE,
+            G_PARAM_READWRITE);
+*/
+
+    properties[PROP_DARK_SCALE] =
+        g_param_spec_float ("dark-scale",
+            "Scale the dark field prior to the flat field correct",
+            "Scale the dark field prior to the flat field correct",
+            -G_MAXFLOAT, G_MAXFLOAT, 1.0f,
+            G_PARAM_READWRITE);
+
+    properties[PROP_FLAT_SCALE] =
+        g_param_spec_float ("flat-scale",
+            "Scale the flat field prior to the flat field correct",
+            "Scale the flat field prior to the flat field correct",
+            -G_MAXFLOAT, G_MAXFLOAT, 1.0f,
+            G_PARAM_READWRITE);
+
+    for (guint i = PROP_0 + 1; i < N_PROPERTIES; i++)
+        g_object_class_install_property (gobject_class, i, properties[i]);
+
+    g_type_class_add_private (gobject_class, sizeof(UfoRoofFlatFieldCorrectTaskPrivate));
+}
+
+static void
+ufo_roof_flat_field_correct_task_init(UfoRoofFlatFieldCorrectTask *self)
+{
+    self->priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE(self);
+    self->priv->fix_nan_and_inf = FALSE;
+    self->priv->absorptivity = FALSE;
+    self->priv->sinogram_input = FALSE;
+    self->priv->kernel = NULL;
+    self->priv->dark_scale = 1.0f;
+    self->priv->flat_scale = 1.0f;
+}
diff --git a/src/ufo-roof-flat-field-correct-task.h b/src/ufo-roof-flat-field-correct-task.h
new file mode 100644
index 0000000..ac82aaa
--- /dev/null
+++ b/src/ufo-roof-flat-field-correct-task.h
@@ -0,0 +1,67 @@
+/*
+ * Copyright (C) 2011-2013 Karlsruhe Institute of Technology
+ *
+ * This file is part of Ufo.
+ *
+ * This library is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef __UFO_ROOF_FLAT_FIELD_CORRECT_TASK_H
+#define __UFO_ROOF_FLAT_FIELD_CORRECT_TASK_H
+
+#include <ufo/ufo.h>
+
+G_BEGIN_DECLS
+
+#define UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK             (ufo_roof_flat_field_correct_task_get_type())
+#define UFO_ROOF_FLAT_FIELD_CORRECT_TASK(obj)             (G_TYPE_CHECK_INSTANCE_CAST((obj), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK, UfoRoofFlatFieldCorrectTask))
+#define UFO_IS_ROOF_FLAT_FIELD_CORRECT_TASK(obj)          (G_TYPE_CHECK_INSTANCE_TYPE((obj), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK))
+#define UFO_ROOF_FLAT_FIELD_CORRECT_TASK_CLASS(klass)     (G_TYPE_CHECK_CLASS_CAST((klass), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK, UfoRoofFlatFieldCorrectTaskClass))
+#define UFO_IS_ROOF_FLAT_FIELD_CORRECT_TASK_CLASS(klass)  (G_TYPE_CHECK_CLASS_TYPE((klass), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK))
+#define UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_CLASS(obj)   (G_TYPE_INSTANCE_GET_CLASS((obj), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK, UfoRoofFlatFieldCorrectTaskClass))
+
+typedef struct _UfoRoofFlatFieldCorrectTask           UfoRoofFlatFieldCorrectTask;
+typedef struct _UfoRoofFlatFieldCorrectTaskClass      UfoRoofFlatFieldCorrectTaskClass;
+typedef struct _UfoRoofFlatFieldCorrectTaskPrivate    UfoRoofFlatFieldCorrectTaskPrivate;
+
+/**
+ * UfoRoofFlatFieldCorrectTask:
+ *
+ * [ADD DESCRIPTION HERE]. The contents of the #UfoRoofFlatFieldCorrectTask structure
+ * are private and should only be accessed via the provided API.
+ */
+struct _UfoRoofFlatFieldCorrectTask {
+    /*< private >*/
+    UfoTaskNode parent_instance;
+
+    UfoRoofFlatFieldCorrectTaskPrivate *priv;
+};
+
+/**
+ * UfoRoofFlatFieldCorrectTaskClass:
+ *
+ * #UfoRoofFlatFieldCorrectTask class
+ */
+struct _UfoRoofFlatFieldCorrectTaskClass {
+    /*< private >*/
+    UfoTaskNodeClass parent_class;
+};
+
+UfoNode  *ufo_roof_flat_field_correct_task_new       (void);
+GType     ufo_roof_flat_field_correct_task_get_type  (void);
+
+G_END_DECLS
+
+#endif
+